Sonic Origins and manuals comparison
Recently, Ian Flynn, English script writer of Sonic Frontiers and writer of the IDW Sonic comics, has said in his podcast that Sonic Origins is now "the canon" of early Sonic games. While this doesn't mean the old Japanese manuals are no longer canon, there are some differences, and, as Ian Flynn said, Origins will be the primary, if not only, point of reference going forward. Apparently, the status of the manuals is currently undecided, and information from past Sonic material may be changed. SEGA recently put together a team dedicated to making a new, consistent foundation for the story and lore of the Sonic series, and these appear to be the first steps towards that.
The most obvious difference between Origins and the old manuals is the use of Mania Adventures style animations as cutscenes. Which means none of the characters are heard talking. This is clearly just an artistic choice, it doesn't mean they're incapable of speaking. However, the original Japanese manuals actually have quite a bit of dialogue, making this a major difference. Generally, the scenes in Origins are much more simplified compared to the original manuals. In this article, I want to explore the differences in more detail.
Sonic the Hedgehog
The animated scenes made for the first game don't give much or any details on the story, unlike the Japanese manual, which explains what South Island is, how the Chaos Emeralds are connected to it, and what the Chaos Emeralds can be used for. The manual also makes it clear Sonic is already familiar with Dr. Eggman, but that this is the first time he put animals inside his robots. All of these details are absent from the introductory scene in Sonic Origins, where Sonic is simply running through Green Hill when he stumbles upon a robot that is attacking some Flickies, and frees the Flicky inside, who then points to Eggman, who has trapped some animals inside a capsule. There is also another small difference. In the manual, Eggman claims all of the animals on the island have been turned into robots, however, two Flickies were already free in Origins.
In the second and final animated scene for the first game, Sonic is in front of the six Chaos Emeralds in Green Hill, surrounded by small animals, and when he touches the green one, the emeralds begin to fly toward Westside Island and are joined by the seventh emerald. This is a nice addition to the end of the game, and nothing like it was in the manual at all, since it only covers the beginning of the story.
Sonic the Hedgehog CD
In the case of Sonic CD, the story portion of the manual is entirely ignored, as the new animated scene focuses on Amy instead. This scene is very close to Amy's character summary from the manual, as it shows her reading her cards before Little Planet appears in her proximity. The manual seems to say that she was the one to go to Little Planet after learning about it from her cards, however the animation is simple and vague enough that it's still possible she had also read her cards beforehand. It does seem weird for her to do it in a field in the open like that though.
Sonic the Hedgehog 2
The Sonic 2 manual gives a backstory for Westside Island, and the first mention of "the gods", who sealed the Chaos Emeralds away after its inhabitants misused them. This is entirely cut from Origins.
In the manual, Tails hides behind a palm tree when Sonic notices him. The manual explains Tails was bullied because of his two tails, however the manual makes no mention of Sonic ever meeting the bullies himself. In the manual, Tails, on his own, is inspired by Sonic. Sonic doesn't do anything other than letting him follow him around. In Origins, it can be said that Sonic simply runs by the newly introduced bully characters, and that this is just yet another simplification to make the animation more immediate, however that is not the only way the scene can be interpreted.
The manual describes Tails finding the Tornado while Sonic is asleep. This is not shown in Origins.
In Origins, Tails realizes he can use his tails to fly by following Sonic. This is an addition that was not present in the manual.
The story in the manual ends with Eggman setting a forest on fire and announcing his plan of world domination with the Death Egg and the Chaos Emeralds. This is also not present in Origins.
Sonic the Hedgehog 3
Like with the other games, Sonic Origins takes a more simplistic approach compared to the Sonic 3 and Sonic & Knuckles manuals. The ending scene isn't even related to Sonic & Knuckles, meaning only the scene between Sonic 2 and Sonic 3 is relevant for this section. The Japanese Sonic 3 manual is the only manual discussed on this page to have received an official English translation, to my knowledge. It focuses on Sonic's side of the story and the legends of Angel Island, while the scene in Origins is about Knuckles meeting Eggman and getting tricked by him. The manual mentions that Sonic 3 takes place many days after Sonic 2, and that mountains and forests were destroyed by the impact of the Death Egg, which also caused Angel Island to fall.
Conclusion
It appears that the Sonic 2 and Sonic 3 manuals are the most affected. While I expect Origins to get continuosly referenced by new Sonic material going forward, which we've already seen happen in Sonic Prime, I would prefer if the original manuals aren't fully ignored. Most of their content can coexist with the animated scenes in Origins, and I think they're an important part of the series' history.